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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagtgcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag

Basic information

species Zea mays
transcript GRMZM5G868433_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 5'ss of exon 2
--GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagt--gcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag---------------
  |||||||| ||||| || |||||||||||||| ||  |||||||||||||||||||||| ||||||| |||| |||| |||||| |||| |||||||||| ||   | | |    || |     ||| ||||    || | |  ||||| ||     | | |  |   | | |   ||||                
AGGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtag

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 3
GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagt--gcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag---------------
|||||||| ||||| || |||||||||||||| ||  |||||||||||||||||||||| ||||||| |||| |||| |||||| |||| |||||||||| ||   | | |    || |     ||| ||||    || | |  ||||| ||     | | |  |   | | |   ||||                
GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtag

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 3
GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagtgcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag--
|||||||| || || ||||| ||||||||||| ||  |||||||||| ||||| ||||| |||||||| || || || |||||| ||||||||||||||||||   |       ||| ||  ||     || |    | | | |    ||     ||   | |||  |      ||     
GAGAAGGAGCTTGTGCAGCTCAAGCGTGAGGCTCGGATGAAGGGTGGGTTCTACGTCAGCCCTGAGGCCAAACTTCTGTTTGTGGTCCGCATCCGTGGgtgagaaac-------tataccgctacggcttaaaattgtctttgtttgcataagcattgacagttcgctatgctttatgtag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15632349|gb|BI679442.1|BI679442
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211173109|gb|FK956294.1|FK956294
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG                         TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG                         TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211173107|gb|FK956292.1|FK956292
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211171435|gb|FK956283.1|FK956283
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211173119|gb|FK956304.1|FK956304
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG                         TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211171440|gb|FK956288.1|FK956288
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG                         TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|20301133|gb|BQ164076.1|BQ164076
EST:     TTCTATGTCAGCCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTA
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTA
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     TTCTATGTCAGCCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|211173112|gb|FK956297.1|FK956297
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGGTCCGCATCCGTGG                         TATCAATGCCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT
genomic: TTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 727

GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 772

GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 634

GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 381

GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgca ... gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagtgcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT